I've run into this issue recently as well. I'm keen to get the Rhode Island Apple Group collection that Jason Scott has been uploading to archive.org into TOSEC, but from what I recall of working on the first batch it's a bit of a mixed bag (had the same issue with the Washington Apple Pi Apple III set). Lots of games and apps, some disks of things like fonts and a few of various games, apps, etc. all piled into one.
On the one hand, it'd be nice to put the unambiguous ones (a disk containing just a cracked version of "Best Apple II Game Ever", for example) into their rightful DATs. On the other, I do feel like there's a benefit of sorts to acknowledging these as all coming from one collection.
I guess unless our metadata gets a bunch more advanced, acknowledging all sorts of extra info and allowing end users to search and sort in various ways, we're going to have to go with compromises. Which is OK, by the way - better to compromise and get things done than get stuck in an endless discussion about the "perfect" way.
Not really contributing anything here, but I'm interested to know what everyone else thinks.